In 2267, Scott, Kirk, Uhura and McCoy were transporting aboard the ISS Enterprise following negotiations on the Halkanhomeworld. While attempting to transport through an ion storm, Scott and crew were exchanged with their counterparts from a mirror universe, and arrived aboard the USS Enterprise, whereas their counterparts arrived aboard the ISS Enterprise. Scott and the three others were immediately placed in the brig of the USS Enterprise, whereas their counterparts were able to somewhat acclimate to life aboard the ISS Enterprise.

There, Scott's counterpart, Montgomery Scott observed how different the ISS Enterprise was from the USS Enterprise, as did that others that transported there with him. (TOS: "Mirror, Mirror")

According to the novel The Sorrows of Empire, this version of Scott was accused of brutally murdering three women on Argelius II, as occurred to his primary universe counterpart in TOS: "Wolf in the Fold". However, Captain Kirk ensured that the charges were dropped without an investigation taking place. Following Kirk's assassination at Spock's hands in 2267, Scott became the ISS Enterprise's first officer. He once again became chief engineer after the ship's refit in 2271, continuing to serve in that position until at least 2287.